Effect of Protein-Polarized Ligand Charges on Relative Protein Ligand Binding Affinities.

A major challenge in computer-aided drug design is predicting relative binding energies of different molecules to a target protein using fast and accurate free-energy calculation methods. Free-energy calculations are primarily computed by utilizing classical molecular dynamics simulations based on all-atom force fields (FF) to model the interactions in the system. The present standard classical all-atom FFs contain fixed partial charges on the atoms, and hence electrostatic interactions are modeled between them.

Absorption spectra of pyruvic acid in water: insights from calculations for small hydrates and comparison to experiment.

Pyruvic acid is abundant in the atmosphere and in seawater, being a decay product of living organisms. Although very small in size (10 atoms), pyruvic acid exhibits conformational complexity in the gas phase and in solution, which is reflected in the UV spectrum. The gas phase UV spectrum of pyruvic acid differs from the spectrum of pyruvic acid in water.

Impact of pH and NaCl and CaCl Salts on the Speciation and Photochemistry of Pyruvic Acid in the Aqueous Phase.

Recent studies have shown that pyruvic acid can produce higher-molecular-weight compounds upon irradiation in the aqueous phase. These compounds can contribute to the formation of secondary organic aerosols. There have been several previous studies on the effect of ionic strength on the photochemistry of pyruvic acid; however, few of them investigated the effects of marine relevant salts such as NaCl and CaCl.

Molecular Dynamics of Photoinduced Reactions of Acrylic Acid: Products, Mechanisms, and Comparison with Experiment.

The photochemistry of acrylic acid is of considerable atmospheric importance. However, the mechanisms and the time scales of the reactions involved are unknown. In this work, the products, yields, and reaction pathways of acrylic acid photochemistry are investigated theoretically by molecular dynamics simulations on the ππ* excited state.

DMAP-assisted sulfonylation as an efficient step for the methylation of primary amine motifs on solid support.

Several multistep strategies were developed to ensure single methylation of amines on solid support. These strategies rely on the introduction of the -NBS protecting/activating group as a key step. We found that the state-of-the-art strategies fail for the methylation of several primary amine motifs, largely due to inefficient sulfonylation.

Photochemistry of Thin Solid Films of the Neonicotinoid Imidacloprid on Surfaces.

Imidacloprid (IMD) is the most widely used neonicotinoid insecticide found on environmental surfaces and in water. Analysis of surface-bound IMD photolysis products was performed using attenuated total reflectance Fourier transfer infrared (ATR-FTIR) analysis, electrospray ionization (ESI-MS), direct analysis in real time mass spectrometry (DART-MS), and transmission FTIR for gas-phase products. Photolysis quantum yields (ϕ) for loss of IMD were determined to be (1.

Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics.

Photochemistry of carbonyl compounds is of major importance in atmospheric and organic chemistry. The photochemistry of cyclohexanone is studied here using on-the-fly molecular dynamics simulations on a semiempirical multireference configuration interaction potential-energy surface to predict the distribution of photoproducts and time scales for their formation. Rich photochemistry is predicted to occur on a picosecond time scale following the photoexcitation of cyclohexanone to the first singlet excited state.

Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces.

CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed.

Photochemistry of aldehyde clusters: cross-molecular versus unimolecular reaction dynamics.

The unimolecular photochemistry of aldehydes has been extensively studied, both experimentally and computationally. However, less is known about the role of cross-molecular photochemical processes in the condensed-phase photolysis of aldehydes. The triplet-state photochemistry of pentanal in its pentameric (n = 5) cluster was investigated as a model for photochemical reactions of aliphatic aldehydes in atmospheric aerosols.

Experimental and theoretical study of aqueous cis-pinonic acid photolysis.

Direct aqueous photolysis of cis-pinonic acid (PA; 2-(3-acetyl-2,2-dimethylcyclobutyl)acetic acid; CAS Registry No. 473-72-3) by 280-400 nm radiation was investigated. The photolysis resulted in Norrish type II isomerization of PA leading to 3-isopropenyl-6-oxoheptanoic acid (CAS Registry No.

Dynamics of triplet-state photochemistry of pentanal: mechanisms of Norrish I, Norrish II, and H abstraction reactions.

The photochemistry of aldehydes in the gas phase has been the topic of extensive studies over the years. However, for all but the smallest aldehydes the dynamics of the processes is largely unknown, and key issues of the mechanisms are open. In this article, the photochemistry of pentanal is studied by dynamics simulation using a semiempirical MRCI code for the singlet and triplet potential energy surfaces involved.

Absorption spectra and photolysis of methyl peroxide in liquid and frozen water.

Methyl peroxide (CH(3)OOH) is commonly found in atmospheric waters and ices in significant concentrations. It is the simplest organic peroxide and an important precursor to hydroxyl radical. Many studies have examined the photochemical behavior of gaseous CH(3)OOH; however, the photochemistry of liquid and frozen water solutions is poorly understood.

Effect of the chirality of residues and γ-turns on the electronic excitation spectra, excited-state reaction paths and conical intersections of capped phenylalanine-alanine dipeptides.

The capped dipeptides Ac-L-Phe-Xxx-NH(2) , Xxx=L-Ala, D-Ala, Aib, where Aib (aminoisobutyric acid) is a non-chiral amino acid, have been investigated by means of UV/IR double-resonance spectroscopy in supersonic jets and density functional theory calculations by Gloaguen et al. [Phys. Chem.

Students with LD in higher education: use and contribution of assistive technology and website courses and their correlation to students' hope and well-being.

This study examined the extent and patterns of usage of web courses, and their contribution to the academic and social perceptions of 964 undergraduate students with and without learning disabilities studying in higher education. Students were asked to complete four questionnaires examining the usage patterns of various adaptive technologies and their contribution to the student. The questionnaires assessed Perceptions of Learning through Online Usage; Accessibility of Campus Computing; Hope Scale and Subjective Well-being Scale.

Role of excited-state hydrogen detachment and hydrogen-transfer processes for the excited-state deactivation of an aromatic dipeptide: N-acetyl tryptophan methyl amide.

The excited-state electronic potential-energy surfaces of the three conformers of the capped dipeptide N-acetyl tryptophan methyl amide (NATMA), for which UV and IR spectra have been reported by Dian et al. [J. Chem.

Efficient excited-state deactivation of the Gly-Phe-Ala tripeptide via an electron-driven proton-transfer process.

Ab initio electronic-structure calculations indicate a mechanism for efficient excited-state deactivation of a low-energy conformer of the Gly-Phe-Ala tripeptide. The particularly short excited-state lifetime can explain the unexpected absence of this conformer in resonant two-photon ionization spectra. It is suggested that these ultrafast electronic deactivation processes provide specific conformers of peptides with a high degree of photostability.

Computational studies of the photophysics of neutral and zwitterionic amino acids in an aqueous environment: tyrosine-(H(2)O)(2) and tryptophan-(H(2)O)(2) clusters.

Tyrosine-(H(2)O)(2) and tryptophan-(H(2)O)(2) clusters have been considered as models for the study of the photochemistry of neutral and zwitterionic tyrosine and tryptophan in an aqueous environment. It has been found that the detachment of neutral NH(3) in the S(1) state of the zwitterionic clusters leads to a low-lying conical intersection of the S(1) and S(0) energy surfaces. This conical intersection can provide the mechanism for efficient radiationless deactivation of the excited state back to the ground state or, alternatively, deamination (loss of ammonia).

Classical trajectory simulations of photoionization dynamics of tryptophan: intramolecular energy flow, hydrogen-transfer processes and conformational transitions.

One-photon and two-photon ionization dynamics of tryptophan is studied by classical trajectory simulations using the semiempirical parametric method number 3 (PM3) potential surface in "on the fly" calculations. The tryptophan conformer is assumed to be in the vibrational ground state prior to ionization. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for that state.

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations.

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered.